Read a text file in R line by line
RTextFile IoR Problem Overview
I would like to read a text file in R, line by line, using a for loop and with the length of the file. The problem is that it only prints character(0). This is the code:
fileName="up_down.txt"
con=file(fileName,open="r")
line=readLines(con)
long=length(line)
for (i in 1:long){
linn=readLines(con,1)
print(linn)
}
close(con)
R Solutions
Solution 1 - R
You should take care with readLines(...) and big files. Reading all lines at memory can be risky. Below is a example of how to read file and process just one line at time:
processFile = function(filepath) {
con = file(filepath, "r")
while ( TRUE ) {
line = readLines(con, n = 1)
if ( length(line) == 0 ) {
break
}
print(line)
}
close(con)
}
Understand the risk of reading a line at memory too. Big files without line breaks can fill your memory too.
Solution 2 - R
Just use readLines on your file:
R> res <- readLines(system.file("DESCRIPTION", package="MASS"))
R> length(res)
[1] 27
R> res
[1] "Package: MASS"
[2] "Priority: recommended"
[3] "Version: 7.3-18"
[4] "Date: 2012-05-28"
[5] "Revision: $Rev: 3167 $"
[6] "Depends: R (>= 2.14.0), grDevices, graphics, stats, utils"
[7] "Suggests: lattice, nlme, nnet, survival"
[8] "Authors@R: c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"),"
[9] " email = \"[email protected]\"), person(\"Kurt\", \"Hornik\", role"
[10] " = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\","
[11] " \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"),"
[12] " person(\"David\", \"Firth\", role = \"ctb\"))"
[13] "Description: Functions and datasets to support Venables and Ripley,"
[14] " 'Modern Applied Statistics with S' (4th edition, 2002)."
[15] "Title: Support Functions and Datasets for Venables and Ripley's MASS"
[16] "License: GPL-2 | GPL-3"
[17] "URL: http://www.stats.ox.ac.uk/pub/MASS4/"
[18] "LazyData: yes"
[19] "Packaged: 2012-05-28 08:47:38 UTC; ripley"
[20] "Author: Brian Ripley [aut, cre, cph], Kurt Hornik [trl] (partial port"
[21] " ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David"
[22] " Firth [ctb]"
[23] "Maintainer: Brian Ripley <[email protected]>"
[24] "Repository: CRAN"
[25] "Date/Publication: 2012-05-28 08:53:03"
[26] "Built: R 2.15.1; x86_64-pc-mingw32; 2012-06-22 14:16:09 UTC; windows"
[27] "Archs: i386, x64"
R>
There is an entire manual devoted to this.
Solution 3 - R
Here is the solution with a for loop. Importantly, it takes the one call to readLines out of the for loop so that it is not improperly called again and again. Here it is:
fileName <- "up_down.txt"
conn <- file(fileName,open="r")
linn <-readLines(conn)
for (i in 1:length(linn)){
print(linn[i])
}
close(conn)
Solution 4 - R
I write a code to read file line by line to meet my demand which different line have different data type follow articles: read-line-by-line-of-a-file-in-r and determining-number-of-linesrecords. And it should be a better solution for big file, I think. My R version (3.3.2).
con = file("pathtotargetfile", "r")
readsizeof<-2 # read size for one step to caculate number of lines in file
nooflines<-0 # number of lines
while((linesread<-length(readLines(con,readsizeof)))>0) # calculate number of lines. Also a better solution for big file
nooflines<-nooflines+linesread
con = file("pathtotargetfile", "r") # open file again to variable con, since the cursor have went to the end of the file after caculating number of lines
typelist = list(0,'c',0,'c',0,0,'c',0) # a list to specific the lines data type, which means the first line has same type with 0 (e.g. numeric)and second line has same type with 'c' (e.g. character). This meet my demand.
for(i in 1:nooflines) {
tmp <- scan(file=con, nlines=1, what=typelist[[i]], quiet=TRUE)
print(is.vector(tmp))
print(tmp)
}
close(con)
Solution 5 - R
I suggest you check out chunked and disk.frame. They both have functions for reading in CSVs chunk-by-chunk.
In particular, disk.frame::csv_to_disk.frame may be the function you are after?
Solution 6 - R
fileName = "up_down.txt"
### code to get the line count of the file
length_connection = pipe(paste("cat ", fileName, " | wc -l", sep = "")) # "cat fileName | wc -l" because that returns just the line count, and NOT the name of the file with it
long = as.numeric(trimws(readLines(con = length_connection, n = 1)))
close(length_connection) # make sure to close the connection
###
for (i in 1:long){
### code to extract a single line at row i from the file
linn_connection_cmd = paste("head -n", format(x = i, scientific = FALSE, big.mark = ""), fileName, "| tail -n 1", sep = " ") # extracts one line from fileName at the desired line number (i)
linn_connection = pipe(linn_connection_cmd)
linn = readLines(con = linn_connection, n = 1)
close(linn_connection) # make sure to close the conection
###
# the line is now loaded into R and anything can be done with it
print(linn)
}
close(con)
By using R's pipe() command, and using shell commands to extract what we want, the full file is never loaded into R, and is read in line by line.
paste("head -n", format(x = i, scientific = FALSE, big.mark = ""), fileName, "| tail -n 1", sep = " ")
It is this command that does all the work; it extracts one line from the desired file.
Edit: R's default behavior is for i to return as normal number when less than 100,000, but begins returning i in scientific notation when it is greater than or equal to 100,000 (1e+05). Thus, format(x = i, scientific = FALSE, big.mark = "") is used in our pipe command to make sure that the pipe() command always receives a number in normal form, which is all that the command can understand. If the pipe() command is given any number like 1e+05, it will not be able to comprehend it and will result in the following error:
head: 1e+05: invalid number of lines